Re: [caret-users] caret 5.3 segmentation of mouse brain
Hi Brige, I am not someone who has had success (or failures) with mouse brain segmentation, but I tried segmenting the map015 left hemisphere using Caret, just to see what would happen. I made these selections: * left the voxel size at 0.056mm * GMpeak=45 ; WMpeak 60 * toggled off disconnect eye and skull and disconnect hindbrain, since these have no chance of working on rodents * toggled on generate segmentation * toggled off fill ventricles, automatic error correction, and all remaining options The idea was to see if I could get an initial segmentation without going any further. The progress bar showed it was working on inner boundary (25%), but then Caret crashed with the following gdb stack trace: Starting program: /146Gb/caret/bin/caret5 [Thread debugging using libthread_db enabled] [New Thread 1085958368 (LWP 14035)] Set the environment variables CARET_DEBUG for debugging information. Program received signal SIGSEGV, Segmentation fault. [Switching to Thread 1085958368 (LWP 14035)] 0x08624da2 in VolumeFile::copyVolumeData (this=0xbfffa640, [EMAIL PROTECTED]) at VolumeFile.cxx:194 194 VolumeFile.cxx: No such file or directory. in VolumeFile.cxx (gdb) where #0 0x08624da2 in VolumeFile::copyVolumeData (this=0xbfffa640, [EMAIL PROTECTED]) at VolumeFile.cxx:194 #1 0x0862428c in VolumeFile::operator= (this=0xbfffa640, [EMAIL PROTECTED]) at VolumeFile.cxx:127 #2 0x0848ca87 in BrainModelVolumeSureFitSegmentation::generateInnerBoundary (this=0xbfffb550) at BrainModelVolumeSureFitSegmentation.cxx:2606 #3 0x0847e9cc in BrainModelVolumeSureFitSegmentation::execute ( this=0xbfffb550) at BrainModelVolumeSureFitSegmentation.cxx:421 #4 0x083312d1 in GuiVolumeSureFitSegmentationDialog::performSegmentation (this=0x9800808) at GuiVolumeSureFitSegmentationDialog.cxx:1405 #5 0x0832e018 in GuiVolumeSureFitSegmentationDialog::next ( this=0x9800808) at GuiVolumeSureFitSegmentationDialog.cxx:936 #6 0x08af5611 in QWizard::qt_invoke () at /usr/local/qt/include/qrect.h:247 #7 0x08351677 in GuiVolumeSureFitSegmentationDialog::qt_invoke ( this=0x9800808, _id=56, _o=0xbfffc990) at moc_GuiVolumeSureFitSegmentationDialog.cpp:114 #8 0x0889ac64 in QObject::activate_signal () at /usr/local/qt/include/qrect.h:247 #9 0x0889a9fb in QObject::activate_signal () at /usr/local/qt/include/qrect.h:247 #10 0x08adcf3e in QButton::clicked () at /usr/local/qt/include/qrect.h:247 #11 0x089120bd in QButton::mouseReleaseEvent () at /usr/local/qt/include/qrect.h:247 #12 0x088c34ed in QWidget::event () at /usr/local/qt/include/qrect.h:247 #13 0x088592bd in QApplication::internalNotify () at /usr/local/qt/include/qrect.h:247 #14 0x08858a90 in QApplication::notify () at /usr/local/qt/include/qrect.h:247 #15 0x08802e6c in QETWidget::translateMouseEvent () at /usr/local/qt/include/qrect.h:247 #16 0x08800eaf in QApplication::x11ProcessEvent () at /usr/local/qt/include/qrect.h:247 #17 0x08afb638 in QEventLoop::processEvents () at /usr/local/qt/include/qrect.h:247 #18 0x088637af in QEventLoop::enterLoop () at /usr/local/qt/include/qrect.h:247 #19 0x08863684 in QEventLoop::exec () at /usr/local/qt/include/qrect.h:247 #20 0x088594a3 in QApplication::exec () at /usr/local/qt/include/qrect.h:247 #21 0x08336918 in main (argc=1, argv=0xbfffe264) at main.cxx:554 (gdb) I knew there were crashing problems when toggling off disconnect hindbrain, but I didn't know what would happen when the other options were also toggled off. We need to look at this and get it working. The idea is to replicate the functionality SureFit had with these selections: segment full volume fill ventricles no skip error correction review surface first skip sulci identification But I don't know how long this will take. Meanwhile, if you're running Linux, you might try using SureFit for this purpose, using the settings above (after doing volume preparation -- orientation, setting AC, cropping, and setting peaks). Donna On 07/29/2005 01:51 PM, Brige Chugh wrote: Hi, I have been trying to apply caret's automatic segmentation routine on the mouse brain. I have registered and resampled the brain so that it is similar to the map015 atlas and have performed n3 correction. I am following the caret segmentation tutorial closely. I am able to clearly discern the grey and white matter peaks but I have found that when I try to run automatic segmentation, it always crashes. The program closes and I get the message segmentation fault. As I new user to the caret environment, I would really appreciate any advice from anyone who has had some success with mouse brain segmentation. Thanks in advance, Brige Paul ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] caret 5.3 segmentation of mouse brain
Brige, The SureFit segmentation algorithm was originally designed for segmenting T1-weighted MRI's of human cerebral cortex, plus other volume data that have similar shape and image intensity attributes. The fundamental requirements are that cortical gray matter be about 3 voxels thick and that white matter be brighter on average and CSF be darker. The hindbrain and cerebellum need customized handling that is species-specific; this is also the case for the olfactory bulb in rodents. The segmentations of mouse and rat cerebral cortex that are the basis of our rodent surface-based atlases (http://sumsdb.wustl.edu:8081/sums/) were done by me personally several years ago; it entailed a large amount of manual editing to achieve a reasonable segmentation. I have not subsequently tried to segment other rodent brains besides the two used for our atlas, nor am I aware of anyone else who has done so using SureFit (or, for that matter, any other algorithm). I would be pleased to have the SureFit algorithm refined so that it works adequately on rodent MRI's. This might well take some additional effort on our part beyond just fixing the crashing problem that you identified and Donna discussed in her email. Once this crash problem is fixed (don't know how long that will take), we will let you know. If you try SureFit/Caret again on the mouse, please keep us posted whether it gives encouraging results or whether specific additional problems arise. David VE On Jul 29, 2005, at 3:15 PM, Donna Hanlon wrote: Hi Brige, I am not someone who has had success (or failures) with mouse brain segmentation, but I tried segmenting the map015 left hemisphere using Caret, just to see what would happen. I made these selections: * left the voxel size at 0.056mm * GMpeak=45 ; WMpeak 60 * toggled off disconnect eye and skull and disconnect hindbrain, since these have no chance of working on rodents * toggled on generate segmentation * toggled off fill ventricles, automatic error correction, and all remaining options The idea was to see if I could get an initial segmentation without going any further. The progress bar showed it was working on inner boundary (25%), but then Caret crashed with the following gdb stack trace: I knew there were crashing problems when toggling off disconnect hindbrain, but I didn't know what would happen when the other options were also toggled off. We need to look at this and get it working. The idea is to replicate the functionality SureFit had with these selections: segment full volume fill ventricles no skip error correction review surface first skip sulci identification But I don't know how long this will take. Meanwhile, if you're running Linux, you might try using SureFit for this purpose, using the settings above (after doing volume preparation -- orientation, setting AC, cropping, and setting peaks). Donna On 07/29/2005 01:51 PM, Brige Chugh wrote: Hi, I have been trying to apply caret's automatic segmentation routine on the mouse brain. I have registered and resampled the brain so that it is similar to the map015 atlas and have performed n3 correction. I am following the caret segmentation tutorial closely. I am able to clearly discern the grey and white matter peaks but I have found that when I try to run automatic segmentation, it always crashes. The program closes and I get the message segmentation fault. As I new user to the caret environment, I would really appreciate any advice from anyone who has had some success with mouse brain segmentation. Thanks in advance, Brige Paul ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
